Ni Hong

Single cell analyses of cancer cells identified two regulatorily and functionally distinct categories in differentially expressed genes among tumor subclones

The paper identifies two distinct categories of differentially expressed genes in tumor subclones based on their regulatory and functional characteristics using single-cell transcriptomic and genomic data from colorectal cancer patients.

The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis

The paper profiles chromatin accessibility dynamics in zebrafish embryos using single-cell ATAC-seq to identify enhancers and transcription factor motifs involved in early cell fate decisions.

Differentiation and migration of hematopoietic stem and progenitor cells cross multiple tissues

The paper integrates single-cell RNA-seq data from multiple tissues to construct a cell atlas of hematopoietic stem and progenitor cells (HSPCs) and identifies migration patterns and signaling interactions involved in their cross-tissue differentiation.

Comprehensive mapping of the alternative polyadenylation site usage and its dynamics at single cell resolution

This study develops scPolyA-seq to analyze alternative polyadenylation at single cell resolution, finding that many genes use only one polyA site per cell and identifying cell cycle-related polyA site usage switches.

ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells

ISSAAC-seq jointly profiles chromatin accessibility and gene expression in single nuclei, revealing cell types, regulatory elements, and chromatin dynamics in mouse cerebral cortex.

Mesenchymal stem cell subpopulations and their heterogeneity of response to inductions revealed by single-cell RNA-seq

The paper identifies MSC subpopulations and their differential responses to inductions using single-cell RNA-seq, revealing subtype-specific gene expression and differentiation potential.

Re-investigation of classic T cell subsets and identification of novel cell subpopulations by single-cell RNA sequencing

The paper re-analyzes T cell subsets using scRNA-seq, identifies new subpopulations, and shows that gene expression patterns define more homogeneous cell populations than surface markers.

Integrated decoding hematopoiesis and leukemogenesis at single-cell resolution and its clinical implication

The paper constructs a single-cell atlas of hematopoiesis and leukemogenesis, identifies leukemia subpopulations, and develops a composite index to predict clinical outcomes.

Principles of 3D Nucleus Organization and Epigenetic Regulation in Diploid Genome Revealed by Multi-omic Data from Hybrid Mouse

The paper uses multi-omic data from hybrid mice to reveal symmetrical positioning of homologous chromosomes in the 3D nucleus and epigenetic regulation differences between B6 and Cast strains.

Exploring the Changing Landscape of Cell-to-Cell Variation After CTCF Knockdown via Single Cell RNA-seq

The paper investigates how CTCF knockdown affects genome-wide cell-to-cell variation using single-cell RNA-seq, finding increased expression noise and enrichment of transcription factor-related genes in CTCF-KD cells.